Out of the six deaths reported, four were from the Nuwera Eliya district in the central highlands which was one of the worst affected areas.
Over 600 people had been evacuated to safe locations while more than 120 houses have been partially or fully damaged.
The Disaster Management Center said that tri forces had been deployed in many of the affected areas and were currently carrying out rescue missions, Xinhua news agency reported.
A landslide warning has also been issued for certain districts, including in Ratnapura, in south central Sri Lanka and those living in landslide prone areas have been warned to vacate immediately.
The Meteorology Department in its latest weather update said more rains were expected in the coming day due to the northeast monsoons establishing over the country.
The areas likely to be the worst affected were the northern and eastern parts of the country while cloudy skies could be expected over other parts of the island.
"General public is kindly requested to take adequate precautions to minimize damages caused by temporary localized strong winds and lightning during thundershowers," the Meteorology Department said.